LOCUS       NM_001397354            1157 bp    mRNA    linear   VRT 19-AUG-2024
DEFINITION  Gallus gallus HOP homeobox (HOPX), transcript variant 5, mRNA.
ACCESSION   NM_001397354
VERSION     NM_001397354.1
KEYWORDS    RefSeq.
SOURCE      Gallus gallus (chicken)
  ORGANISM  Gallus gallus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
            Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes;
            Phasianidae; Phasianinae; Gallus.
REFERENCE   1  (bases 1 to 1157)
  AUTHORS   Tang,H., Finn,R.D. and Thomas,P.D.
  TITLE     TreeGrafter: phylogenetic tree-based annotation of proteins with
            Gene Ontology terms and other annotations
  JOURNAL   Bioinformatics 35 (3), 518-520 (2019)
   PUBMED   30032202
REFERENCE   2  (bases 1 to 1157)
  AUTHORS   Kovarova,D., Plachy,J., Kosla,J., Trejbalova,K., Cermak,V. and
            Hejnar,J.
  TITLE     Downregulation of HOPX controls metastatic behavior in sarcoma
            cells and identifies genes associated with metastasis
  JOURNAL   Mol Cancer Res 11 (10), 1235-1247 (2013)
   PUBMED   23938949
  REMARK    GeneRIF: Data demonstrate that HOPX is a metastasis-associated gene
            and that its knockdown decreases the metastatic activity of
            v-src-transformed cells through altered gene expression patterns.
REFERENCE   3  (bases 1 to 1157)
  AUTHORS   Burge,S., Kelly,E., Lonsdale,D., Mutowo-Muellenet,P., McAnulla,C.,
            Mitchell,A., Sangrador-Vegas,A., Yong,S.Y., Mulder,N. and Hunter,S.
  TITLE     Manual GO annotation of predictive protein signatures: the InterPro
            approach to GO curation
  JOURNAL   Database (Oxford) 2012, bar068 (2012)
   PUBMED   22301074
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 1157)
  AUTHORS   Vasiliev,O., Rhodes,S.J. and Beebe,D.C.
  TITLE     Identification and expression of Hop, an atypical homeobox gene
            expressed late in lens fiber cell terminal differentiation
  JOURNAL   Mol Vis 13, 114-124 (2007)
   PUBMED   17277742
  REMARK    GeneRIF: Expression pattern of Hop provides first evidence that new
            transcription is initiated in lens fiber cells after they detach
            from the capsule. Hop may be first of class of genes with this
            pattern of expression.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1157)
  AUTHORS   Adu,J., Leong,F.T., Smith,N.R., Leek,J.P., Markham,A.F.,
            Robinson,P.A. and Mighell,A.J.
  TITLE     Expression of mOb1, a novel atypical 73 amino acid K50-homeodomain
            protein, during mouse development
  JOURNAL   Mech Dev 119 Suppl 1, S43-S47 (2002)
   PUBMED   14516659
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAENSK010000074.1.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR12888486.102165.1,
                                           SRR12888488.97931.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN02738218, SAMN02738221
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-120               JAENSK010000074.1  1816107-1816226     c
            121-216             JAENSK010000074.1  1815872-1815967     c
            217-298             JAENSK010000074.1  1812777-1812858     c
            299-467             JAENSK010000074.1  1810280-1810448     c
            468-1157            JAENSK010000074.1  1807464-1808153     c
FEATURES             Location/Qualifiers
     source          1..1157
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="4"
                     /map="4"
     gene            1..1157
                     /gene="HOPX"
                     /gene_synonym="HOD; HOP; OB1"
                     /note="HOP homeobox"
                     /db_xref="CGNC:8667"
                     /db_xref="GeneID:395241"
     exon            1..120
                     /gene="HOPX"
                     /gene_synonym="HOD; HOP; OB1"
                     /inference="alignment:Splign:2.1.0"
     exon            121..216
                     /gene="HOPX"
                     /gene_synonym="HOD; HOP; OB1"
                     /inference="alignment:Splign:2.1.0"
     exon            217..298
                     /gene="HOPX"
                     /gene_synonym="HOD; HOP; OB1"
                     /inference="alignment:Splign:2.1.0"
     exon            299..467
                     /gene="HOPX"
                     /gene_synonym="HOD; HOP; OB1"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    303..305
                     /gene="HOPX"
                     /gene_synonym="HOD; HOP; OB1"
                     /note="upstream in-frame stop codon"
     CDS             324..545
                     /gene="HOPX"
                     /gene_synonym="HOD; HOP; OB1"
                     /note="odd homeobox 1 protein; odd homeobox protein 1"
                     /codon_start=1
                     /product="homeodomain-only protein"
                     /protein_id="NP_001384283.1"
                     /db_xref="CGNC:8667"
                     /db_xref="GeneID:395241"
                     /translation="

MATEKSVTPTEEQLEILEYNFCKVNKHPDPTTLCLIAAETGLSEEQTLKWFKQRLAEWRKSEGLPSECGSVRD"

     misc_feature    336..509
                     /gene="HOPX"
                     /gene_synonym="HOD; HOP; OB1"
                     /note="Homeodomain; DNA binding domains involved in the
                     transcriptional regulation of key eukaryotic developmental
                     processes; may bind to DNA as monomers or as homo- and/or
                     heterodimers, in a sequence-specific manner; Region:
                     homeodomain; cd00086"
                     /db_xref="CDD:238039"
     misc_feature    order(336..344,348..350,402..404,420..422,459..461,
                     465..470,477..482,486..494,498..503)
                     /gene="HOPX"
                     /gene_synonym="HOD; HOP; OB1"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(336..338,345..347,468..470,477..482,489..491)
                     /gene="HOPX"
                     /gene_synonym="HOD; HOP; OB1"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            468..1157
                     /gene="HOPX"
                     /gene_synonym="HOD; HOP; OB1"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gcactttttcccctgaaggaaggaagactccttgatgggcctggaggcagtctgcatgctgtttctttaatctgactctcctgtcaaagggactgcatctggggccaggatattttccaggactcccagcagctctgataccatttcagtggcacgtctcagcctgaaatacttcactgccagcgctccctgtgcaagtctgggctggattcagagaaaaataagctagcggtggtgcctttcagcagttgagcagaacagttgtgattctccatcttcctgccaggcttaaagaaagtgcctgaccccaccatccaggagaaatggccacggagaagtcagtgactcctactgaggagcagctagagatcctggagtacaatttttgcaaggtgaacaagcatcctgatcccaccacgctgtgcctcattgcagctgagaccgggctttctgaagagcagaccctgaaatggttcaagcagcgcctggcagagtggaggaagtctgaagggctgccctcagaatgtgggtctgtgagggactagaggatgctgctcctggccccatccatgctgtaaacgatggtgaagatcttcagagtgggtttacttggggttctcctgtcacaaaaggtttcaagatacaaagcaataccctgatatttaacataatttttatttatagaagattatatatatataatatgtatgtatatgtgtatacagctcctgatggctgcataacttgtctagcaattcccattaatagcagctgcacaggccaggaaatctcatgcccttgtcctgggctcatggaaaagctgccaagaaaggatcaagcacaggagggaggaatagagatttcttttccctatgatcccaagaggcaaagcatgcatgctagctttagtatatagagcatccagaaaggagggcaattggaaaacttgatgtcttgatcttgtgatgtcttggttagtttaaggtgcccaagccagctctggatattgacaagctaagagcctacatcattaacagactgagccaagatcctttgaatgtatgtctcacatttctgttaaagatcaccgaagggagagaactggtcttttctttgtccaaagtgtgaataaaaaccaaagatttttggtgagagaa

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